This option is especially useful when dealing with source CID spectra. If you have a library which consists exclusively of source CID spectra and your unknown spectrum is also a source CID, other spectra types should be excluded from a search. If no such library is available, you can search source CID spectra in product CID spectra, but you should be careful regarding the search results. Source CID spectra may contain fragmentation products from all the ions present in the source including adduct or cluster ions, while product CID spectra are preferably generated from protonated or deprotonated ions.

There are two combinations relating to the tree search:

• Search single spectrum in library trees
  
  
• Search tree in library trees

If you search a single spectrum in library trees, the spectrum will be compared to every spectrum in tree hierarchy and the match factor will be individually calculated. A single spectrum can be searched in the top level only (full scan, source CID), or everywhere except for the top level (first stage), or everywhere in the tree:

If you search a tree (unknown) against spectral trees in a library, the spectrum will be compared according to a special logic. The corresponding spectra on an identical level (MSⁿ stage) with a common precursor m/z are compared using an algorithm based on the optimized dot-product. If a spectrum only appears on one side, it will be ignored and will not negatively effect the search result. If there are several corresponding spectra (single node with average, composite, parallel or other spectra), the best match is accepted (optimistic approach). The total match factor is calculated from all the non-zero match factors.

A spectral tree can be searched using two options. The top tree level (full scan, source CID) can be included or excluded from a search and the MSⁿ stage of the tree spectra can be identical (identity search) or not identical (sub-tree search):

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